tools/protein_tools/scripts/score_vs_rmsCore.R
- Create a score vs. RMSD scatter plot from a score file. The RMSD is calculated for the protein core region and the scorefile must contain a 'rms_core' column.

tools/protein_tools/scripts/score_vs_rmsTM.R
- Create a score vs. RMSD scatter plot from a score file. The RMSD is calculated for the protein transmembrane region and the scorefile must contain a 'rms_TM' column.

tools/analysis/numeric/MultiDimensionalHistogram.R
-

tools/analysis/protocols/moves/DOFHistogramRecorder.R
-

tools/analysis/constraints/score_vs_atom_pair_constraint.R
- Make a total score vs. atom_pair_constraint scatter plot.

Epitope Prediction Tools

We have provided tools to predict epitopes using Propred matrices or NetMHCII, and also to create databases to allow sequences to be evaluated quickly in Rosetta. See MHCEpitopeEnergy for more details on immunogenicity scoring in Rosetta. See the tools documentation for details on how to use the mhc_energy_tools.

tools/mhc_energy_tools/mhc_score.py to perform epitope scoring on FASTA, PDB, or raw peptides, with basic reporting and plotting capabilities.
tools/mhc_energy_tools/mhc_gen_db.py to generate SQL databases from FASTA or PDB files, with design space being specified from a CSV file or a PSSM.

AMBRose (AMBER molecular dynamics intercompatibility)

AMBRose is a PyRosetta package for easily working with AMBER. Its documentation can be found here, and the package itself is found at tools/AmbRose/ambrose.